Malnutrition is a huge problem in Burundi. In order to improve the health system response, the Ministry of Health piloted the introduction of malnutrition prevention and care indicators within its performance-based financing (PBF) scheme. Paying for units of services and for qualitative indicators is expected to enhance provision and quality of these nutrition services. The objective of this study is to assess the impacts of this intervention, on both child acute malnutrition recovery rates at health centre level and prevalence of chronic and acute malnutrition among children at community level. This study follows a cluster-randomized controlled evaluation design: 90 health centres (HC) were randomly selected for the study, 45 of them were randomly assigned to the intervention and received payment related to their performance in malnutrition activities, while the other 45 constituted the control group and got a simple budget allocation. Data were collected from baseline and follow-up surveys of the 90 health centres and 6,480 households with children aged 6 to 23 months. From the respectively 1,067 and 1,402 moderate and severe acute malnutrition transcribed files and registers, findings suggest that the intervention had a positive impact on moderate acute malnutrition recovery rates (OR: 5.59, p = 0.039-at the endline, 78% in the control group and 97% in the intervention group) but not on uncomplicated severe acute malnutrition recovery rate (OR: 1.16, p = 0.751-at the endline, 93% in the control group and 92% in the intervention group). The intervention also had a significant increasing impact on the number of children treated for acute malnutrition. Analyses from the anthropometric data collected among 12,679 children aged 6-23 months suggest improvements at health centre level did not translate into better results at community level: prevalence of both acute and chronic malnutrition remained high, precisely at the endline, acute and chronic malnutrition prevalence were resp. 8.80% and 49.90% in the control group and 8.70% and 52.0% in the intervention group, the differences being non-significant. PBF can contribute to a better